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UMRAM and Bilkent University Department of Psychology has a new faculty member: Dr. Burcu Ayşen Ürgen Burcu Ayşen Ürgen received her PhD in Cognitive Science from University of California, San Diego (USA) in 2015. Prior to her PhD, she did her BS in Computer Engineering at Bilkent University, and MS in Cognitive Science at Middle East Technical University. Following her PhD, she worked as a postdoctoral researcher at the Department of Neuroscience, University of Parma (Italy), with Professor Guy A. Orban. Dr. Ürgen’s primary research area is human visual perception with a focus on biological motion and action perception. In addition to behavioral methods, she uses a wide range of invasive and non-invasive neuroimaging techniques including fMRI, EEG, and intracranial recordings to study the neural basis of visual perception. Her research commonly utilizes state-of-the-art computational techniques including machine learning, computer vision, and effective connectivity. Besides her basic cognitive neuroscience research, Dr. Ürgen also pursues an interdisciplinary research between social robotics and cognitive neuroscience to investigate the human factors that lead to successful interaction with artificial agents such as robots. For profile: https://umram.bilkent.edu.tr/index.php/teams/burcu-ayse-urgen/  Personal website: http://burcu.urgen.bilkent.edu.tr Lab website: http://www.ccn.bilkent.edu.tr

Görkem Er, from UMRAM, has successfully defended his MSc thesis on September 13th, 2018. He is currently enrolled in Neuroscience Master program with his supervisor Hüseyin Boyacı at Bilkent University.   Thesis Title: The Role of Contrast and Size In Motion Perception: Behavioral And Neuroimaging Study Of Center-Surround Interactions In Primary Visual Cortex (V1) And Middle Temporal Area (MT+). Abstract: Behavioral experiments have demonstrated that observers’ ability to discriminate the drift direction of a grating improves as its size increases if the grating has a low contrast, and deteriorates if it has a high contrast [1]. It has been proposed that receptive field organization in middle temporal (MT+) visual area underlies this counter-intuitive perceptual effect. Supporting evidence for this proposal has been provided in literature [2]. However, previous studies have not unequivocally showed that MT+ is the sole area whose activity underlies the perceptual effect. Here, we investigate the activity patterns of primary visual cortex (V1) and middle temporal (MT+) in response to drifting Gabor patches in differing size and contrast levels to elucidate the neural region involved in size-contrast interac- tion in motion perception. We first replicated the findings in the literature with a behavioral experiment, where small or large (1.67 and 8.05 degrees of visual angle) drifting gratings with either low (2%) or high (99%) contrast levels were presented at the periphery (centered 9.06 degrees of visual angle to left and right of fixation). We measured the duration thresholds (79%) for accurately discrim- inating the drift direction of gratings for eleven participants using an adaptive staircase and two-alternative forced choice (2AFC) design. In line with previous literature, we observed that increasing the size of the low-contrast stimuli resulted in decreased discrimination threshold, while for high-contrast stimuli, increasing the size resulted in increased discrimination threshold. In the second stage of the study, six observers participated in a block design fMRI study with the same spatial configuration and contrast levels used in the behavioral experiment. We first identified the region of interests (ROI) for visual area V1 and MT+ separately for all participants. Then, we identified a ”sub-ROI” that corresponds to the region that was selectively responsive to the small sized stimuli (1.67 degrees) using an independent localizer. With this setup, we allowed for both large and small sized gratings to stimulate the sub-ROI throughout the entire scan. Therefore, changes in Blood Oxygenated Level Dependent (BOLD) response at the sub-ROI in response to large compared to small sized gratings indicated the influence of the surrounding region to the center of the gratings. In area MT+, we observed that increasing the size of the grating increases the BOLD activity if the stimuli have low contrast, compared to high contrast. In other words, surrounding region had a facilitative influence to the group of MT+ neurons encoding the center of the stimuli if the stimuli had low contrast. This neuronal facilitation observed with the neuroimaging data explain the enhance- ment of the performance with increasing the size of the low-contrasted stimuli observed at the behavioral experiment. In V1, however, increasing the size of the high-contrasted gratings increased the BOLD activity, compared to activity evoked by increasing the size of the low-contrasted gratings. On the whole, we show that center-surround interaction in V1 and MT were differentiated in re- sponse to peripherally viewed drifting Gabor patches at differing contrast and size levels, hence we provide further evidence that the perceptual size-contrast interaction effect is likely to originates at cortical area MT+.

Our New Web Site is Published!

UMRAM website https://umram.bilkent.edu.tr is now online with its new face! In order to provide better service in the academic and technological sense, our website, which is full of innovations, has been published. You can access up-to-date news, academic publications, projects, past and future events and conferences, detailed personal pages and recent UMRAM photos.

Mert Hidayetoglu of University of Illinois at Urbana Champain presented on his PhD studies.

Talk was entitled “SUPERCOMPUTING FOR FULL-WAVE TOMOGRAPHIC IMAGE RECONSTRUCTION IN NEAR-REAL TIME.”

The abstract of the talk is:

Full-wave methods incorporate all wave phenomena into the image reconstructions by solving the Helmholtz equation with no fundamental approximation. These phenomena include refraction, absorption, diffraction, and multiple-scattering of propagating waves.  Although full-wave image reconstruction has promising features and can lead to new imaging technologies, it has been regarded as impractical due to its high computational burden.  This talk will be on our effort of making full-wave imaging attainable with two approaches:  fast algorithms and supercomputing. We formulate image reconstruction as inverse multiple-scattering problem which is solved by nonlinear optimization method. The mathematically-exact functional derivative is found with the distorted-Born approximation.  However, a large image reconstruction requires solving hundreds of thousands of forward-scattering problems, i.e., inversion of large _N_-by-_N_ dense matrices.  As a remedy, we employ the multilevel fast multipole algorithm for solving these forward problems with O(_N_) computational complexity.  Furthermore, we use NCSA’s Blue Waters supercomputing facility with CPU+GPU node architecture for massively-parallel reconstructions.  For efficient implementation, we seek low-level GPU optimizations and effective heterogeneous computing. This talk provides an overview of computational methods, efficient parallelization strategies on large supercomputers, some GPU optimizations, and performance results.  Results show good scaling up to 4,096 GPU nodes which provides the largest full-wave image reconstructions to date in near-real time. Several real-life scenarios will be provided where the proposed methodology is especially useful and outperforms conventional approaches in terms of image quality. Shirt bio of Mert Hidayetoglu: Mert Hidayetoglu is a Ph.D. candidate ECE Illinois, where he works with Prof. Weng Cho Chew and Prof. Wen-Mei Hwu. Mert’s research interests include electromagnetics, fast algorithms for integral-equation methods, inverse scattering and imaging, and parallel & high-performance computing. He is among the first two authors of more than a dozen of conference papers and of several journal papers. He was awarded with the professor Kung Chie Yeh and Dan Vivoli endowed fellowships by the ECE department, and with computational science and engineering fellowship by the college of engineering at Illinois. Recently, he won the second place at the 2018 IEEE IPDPS Ph.D. Forum poster competition by popular vote. In Summer 2018, he was a Givens fellow at Argonne National Laboratory.

ASELSAN’dan 2 milyar dolarlık hamle ASELSAN, dışa bağımlılığın yüzde 85 olduğu ve yılda 2 milyar dolar ithalata yol açan medikal cihaz ve bileşenleri için yerli ve milli çözümler geliştiriyor.

Türkiye’nin teknoloji merkezlerinden ASELSAN, yerli tıbbi cihazların geliştirilmesi ve bu alandaki yurt dışı bağımlılığın azaltılması için çok yönlü çalışma yürütüyor.

Türkiye’de sağlık teknolojilerindeki dışa bağımlılık yüzde 85 düzeyinde bulunuyor ve bu alanda yılda 2 milyar dolarlık ithalat gerçekleştiriliyor. Yerli üreticiler ise ileri teknoloji gerektirmeyen, katma değeri düşük ürünlere yöneliyor. Bakım-onarım anlaşmaları, sarf malzeme ihtiyacı ve yazılım güncelleme masraflarıyla medikal cihazların maliyet yükü artıyor.

Savunma ve sağlık, teknolojik olarak birbirini besleyebilecek iki önemli sanayi kolu olarak dikkati çekiyor. Bu alanlarda temel teknolojilerin çift amaçlı (dual-use) kullanımıyla yaygın şekilde karşılaşılıyor. Bu nedenle ASELSAN’ın savunma alanında sahip olduğu teknolojilerle medikal cihaz ve bileşenlerini yerli ve milli geliştirebileceği değerlendirilerek, şirketin faaliyet alanına sağlık teknolojileri de eklendi.

Sağlık teknolojileri alanındaki öncelikli faaliyet konusu, içerdiği teknolojilerin ASELSAN’ın tecrübeli olduğu alanlarla ortak olması göz önünde bulundurularak “medikal görüntüleme sistemleri” olarak belirlendi.

Sağlık Bakanlığı, manyetik rezonans (MR) görüntüleme, bilgisayarlı tomografi, ultrasonografi, dijital röntgen cihazlarının yerlileştirilmesiyle ilgili bir projeyi hayata geçirmek için çaba sarf ediyor. ASELSAN da sağlık endüstrisi açısından çok önemli olan bu proje kapsamında savunmada edindiği tecrübeyi, sağlık endüstrisi ekosistemiyle çalışarak ülkenin hizmetine sunmayı hedefliyor.

ASELSAN, bu projeye hazırlık olması amacıyla öz kaynaklarıyla “mobil dijital röntgen” ve “yerli MR görüntüleme sistemi” geliştirilmesi projelerini başlattı. Gelecek yıl ürünlerin ilk örneklerinin çıkarılmasına yönelik çalışmalar devam ediyor.

Yerli ürünler için yeni iş birlikleri

ASELSAN, bu projelere ek olarak, Türkiye’nin sağlık ekosisteminde faaliyet gösteren yetkin ve start-up firmalarıyla beraber çalışma olanaklarını değerlendiriyor. Bu doğrultuda, defibrilatör (elektroşok) cihazlarında iş birliği yapmak üzere ilk adım atıldı. Bu adımı yaşam destek cihazlarında yapılacak diğer iş birlikleri izleyecek.

ASELSAN’ın mühendislik, yüksek teknolojili ürün geliştirme ve kalite yönetimi kabiliyetleriyle iş birliği yapılan firmaların alan uzmanlığı bir araya getirilecek, yenilikçi ve uluslararası pazarda iddialı ürünlerin yerli imkanlarla üretimi gerçekleştirilecek. Tıbbi cihaz alanında, Türkiye içinde benzer iş birlikleri artırılarak devam edecek.

Haberin tamamına buradan ulaşabilirsiniz: https://www.aa.com.tr/tr/ekonomi/aselsandan-2-milyar-dolarlik-hamle/1249716 Kaynak: Anadolu Ajansı

Dr. Gene R. Stoner (Visiting Faculty) and his colleagues at UMRAM published a research article in Journal of Neurophysiology. In their study, they utilized a set of audiovisual stimuli that elicit an illusion demonstrating “temporal ventriloquism” in visual motion and that have spatiotemporal intervals for which neurons within area MT are selective. They found evidence of auditory input into area MT but not of the non-linear audiovisual interactions underlying this illusion. Click here for further information and the journal article.

Serhat Ilbey has successfully defended his MSc thesis on April 20th, 2018. The title of his thesis is “FAST CALIBRATION AND IMAGE RECONSTRUCTION FOR MAGNETIC PARTICLE IMAGING”. This thesis work is the result of a collaborative project between UMRAM and ASELSAN, co-advised by Asst. Prof. Emine Ulku Saritas and Dr. Can Baris Top. This thesis proposes using coded calibration scenes and compressed sensing methods to highly accelerate the otherwise lengthy calibration scans needed for high quality image reconstruction in Magnetic Particle Imaging. Serhat will continue his Ph.D. studies at UMRAM.

The paper titled “Joint Partial Fourier and Compressed Sensing Reconstruction for Accelerated Time-of-Flight MR Angiography” authored by our graduate students and faculty members, Toygan Kılıç, Asst. Prof. Tolga Çukur, Prof. Oktay Algın, and Asst. Prof. Emine Ülkü Sarıtaş, has received IEEE EMBS Turkey The Best Student Paper Award at the 26th IEEE Signal Processing and Communications Applications Conference.

Mustafa Can Delikanlı was granted the best oral presentation award at the 13th National Radiotechnology Congress and Training Seminars The presentation by Mustafa Can Delikanlı was selected as the best oral presentation  at the 13th National Radiotechnology Congress and Training Seminars organized by the Turkish Medical Radiotechnology Department in Cyprus which is held between 23-26 April 2018. The “RAT COIL” report prepared in UMRAM Laboratories was selected the  best among 60 presentations.  Instead of a plaque of thanks,  a sapling planted in Gaziantep Nurdağı Memorial Forest. We congratulate Mustafa Can Delikanlı for his success in the event.

Dr. Oktay Algin of Yilidirim Beyazit University became professor. CONGRATULATIONS. Radiologist Dr. Algin is an adjunct faculty member of UMRAM. He co-authored many publications with UMRAM researchers including “Alipour, A., Gokyar, S., Algin, O., Atalar, E. and Demir, H.V., An inductively coupled ultra-thin, flexible and passive RF resonator for MRI marking and guiding purposes: clinical feasibility in Magnetic Resonance in Medicine 2018, 80:361-370.” and “Silemek, B., Acikel, V., Oto, C., Alipour, A., Aykut, Z.G., Algin, O. and Atalar, E., A Temperature Sensor Implant for Active Implantable Medical Devices for In Vivo Subacute Heating Tests Under MRI in Magnetic Resonance in Medicine 2018, 79:2824-2832.” Dr. Algin is known for his work on hydrocephalus.

Professor Oktay Algın has been given Turkan Saylan Science Award by  the Academy of Association for Supporting Contemporary Life. This award is given to the young academics with outstanding achievements. Turkan Saylan is an important character in Turkish Medical History who has helped to fought and overcome leprosy in Turkey. She was an influencial Turkish doctor who touched so many people’s lives in so many varied ways. This prize is given every year on the anniversary of her death to the young scientists who would carry her name and understanding of contemporary life style into the future. We congratulate Dr Algın for receiving such meaningful and important award and wish him our best in the future.

Sevgi Gokce Kafali has successfully defended her MSc thesis on April 17th, 2018. The title of her thesis is “PHASE-CORRECTING DENOISING FOR DIFFUSION MAGNETIC RESONANCE IMAGING.” This work proposes a simultaneous solution to low-SNR and motion-induced phase problems experienced in diffusion MRI, via a novel phase-correcting non-local means (PC-NLM) filter. Sevgi’s first-author paper on this work was recently published in Magnetic Resonance in Medicine (see this link). Sevgi will join University of California, Los Angeles (UCLA) in September for her PhD studies.